A quantitative, genome-wide analysis in<i>Drosophila</i>reveals transposable elements’ influence on gene expression is species-specific

Fablet, Marie; Salces-Ortiz, Judit; Jacquet, Angelo; Menezes, Bianca Fraga; Dechaud, Corentin; Veber, Philippe; Noûs, Camille; Rebollo, Rita; Vieira, Cristina

doi:10.1101/2022.01.20.477049

Cited by 2 publications

(8 citation statements)

References 79 publications

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“…Genome assembly has been deposited in the European Nucleotide Archive (ENA) under accession number PRJEB50024, assembly GCA_927717585.1. Gene annotation was performed as described in (Fablet et al, 2023). Briefly, gene annotation files were retrieved from Flybase (dmel-all-r6.46.gtf.gz) along with the matching genome sequence (fasta/dmel-all-chromosome-r6.46.fasta.gz).…”

Section: Reference Genome and Annotationmentioning

confidence: 99%

“…We then extracted the dinucleotides flanking the gap on the reference sequence. Scripts used are available on the git repository (SplicingAnalysis.py, splicing_analysis.sh) Short-read RNA-seq and analysis RNA extraction and short-read sequencing were retrieved either from (Fablet et al, 2023), at the NCBI BioProject database PRJNA795668 (SRX13669659 and SRX13669658), or performed here and available at BioProject PRJNA981353 (SRX20759708, SRX20759707). Briefly, RNA was extracted from 70 testes and 30 ovaries from adults aged three to five days, using RNeasy Plus (Qiagen) kit following the manufacturer's instructions.…”

Section: Splicingmentioning

confidence: 99%

“…Genome assembly has been deposited in the European Nucleotide Archive (ENA) under accession number PRJEB50024. Gene annotation was performed as described in (Fablet et al, 2022). Briefly, we used LiftOff (Shumate & Salzberg, 2021) on FlyBase D. melanogaster annotation (dmel-all-r6.46.gtf.gz), with the option -flank 0.2.…”

Section: Reference Genome and Annotationmentioning

confidence: 99%

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Identification and quantification of transposable element transcripts using Long-Read RNA-seq inDrosophilagermline tissues

Rebollo

Cumunel

Mary

et al. 2023

Preprint

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Transposable elements (TEs) are repeated DNA sequences potentially able to move throughout the genome. In addition to their inherent mutagenic effects, TEs are also able to disrupt nearby genes by donating their intrinsic regulatory sequences, as for instance, promoting the ectopic expression of a cellular gene. TE transcription is therefore not only necessary for TE transpositionper sebut can also be associated with TE-gene fusion transcripts, and in some cases, be the product of pervasive transcription. Hence, correctly determining the transcription state of a TE copy is essential to apprehend the impact of the TE in the host genome. Methods to identify and quantify TE transcription have mostly relied on short RNAseq reads to estimate TE expression at the family level, while using specific algorithms to try to discriminate copy-specific transcription. However, assigning short reads to their correct genomic location, and genomic feature is not trivial. Here we retrieved full-length cDNA (TeloPrime, Lexogen) ofDrosophila melanogastergonads and sequenced them using Oxford Nanopore Technologies. We show that long-read RNAseq can be used to identify and quantify TEs at the copy level. In particular, TE insertions overlapping annotated genes are better estimated using long-reads than short-reads. Nevertheless, long TE transcripts (> 5kb) are not well captured. Most expressed TE insertions correspond to copies that have lost their ability to transpose. Some TEs exhibit interesting patterns, such as intronic POGO sequences, which are expressed in ovaries and not testes, in opposition to the host gene. In many instances, we see that TEs can be spliced, independent of their structure or class. Overall, this first comparison of TEs between testis and ovaries uncovers differences in their transcriptional landscape, at the subclass and insertion level.

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Section: Reference Genome and Annotationmentioning

confidence: 99%

Section: Splicingmentioning

confidence: 99%

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Identification and quantification of transposable element transcripts using Long-Read RNA-seq inDrosophilagermline tissues

Rebollo

Cumunel

Mary

et al. 2023

Preprint

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“…ChimeraTE mode 1 was run on the four wild-type strain genomes and their respective ovarian RNA-seq data (63). Across all strains, we found 506 genes producing chimeric transcripts, representing 2.83% of the total genes in D. melanogaster and 6.15% of the expressed genes (FPKM >1).…”

Section: Resultsmentioning

confidence: 99%

“…In order to assess ChimeraTE's performance, as well as the efficiency in the identification of chimeric transcripts derived from polymorphic TE insertions, we have mined previously available RNA-seq data from four D. melanogaster wild-type strains (50). Two from France, Gotheron (44_56'0"N 04_53'30"E), named dmgoth101 and dmgoth63; and two from Brazil, São José do Rio Preto (20_41'04.3"S 49_21'26.1"W), named dmsj23 and dmsj7.…”

Section: Melanogaster Wild-type Strains: Genome Assemblies and Rna-seqmentioning

confidence: 99%

ChimeraTE: A pipeline to detect chimeric transcripts derived from genes and transposable elements

Oliveira

Fablet

Larue

et al. 2022

Preprint

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Transposable elements (TEs) are structural variants considered an important source of genetic diversity, which may arise in the transcriptome when TEs are transcribed in the same RNA molecule as genes, producing what we hereafter call chimeric transcripts. The presence of chimeric transcripts has been associated with adaptive traits in several species, but their identification remains hindered due to the lack of tools to detect them on a transcriptome-wide scale. Previous bioinformatics tools were developed to identify chimeric transcripts derived from TEs present in a reference genome. Nevertheless, different individuals/cells/strains might harbor different TE insertions generating such chimeric transcripts. Therefore, we have developed ChimeraTE, a pipeline that uses paired-end RNA-seq reads to identify chimeric transcripts with or without a reference genome, in a transcriptome-wide manner. ChimeraTE has two Modes: Mode 1 is a genome-guided approach that employs the canonical method of genome alignment, whereas Mode 2 identifies chimeric transcripts without a reference genome, being able to predict chimeras derived from fixed or polymorphic TEs. We have used both Modes with Illumina RNA-seq reads from ovarian tissues of Drosophila melanogaster wild-type strains, and found that ~3% of all genes generate chimeric transcripts. Approximately ~9% of all detected chimeras were absent from the D. melanogaster′s reference genome, corresponding to polymorphic insertions in the wild-type strains. ChimeraTE is the first pipeline with the ability to automatically uncover chimeric transcripts without a reference genome.

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A quantitative, genome-wide analysis inDrosophilareveals transposable elements’ influence on gene expression is species-specific

Cited by 2 publications

References 79 publications

Identification and quantification of transposable element transcripts using Long-Read RNA-seq inDrosophilagermline tissues

Identification and quantification of transposable element transcripts using Long-Read RNA-seq inDrosophilagermline tissues

ChimeraTE: A pipeline to detect chimeric transcripts derived from genes and transposable elements

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